Aside

Contact

brian_schilder [at] alumni.brown.edu
US
+1 908-268-9859
UK
+44 073-0653-7736
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GitHub
Twitter
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Personal Website
Lab Website

Summary

16+ years of research
24 publications
7 preprints
41 software packages
11 databases & apps
23 talks
14+ years of teaching & team management

Table of Contents

Education
Skills
Publications
Preprints
Experience
Grants


Updated Mar-18-2025
header_img Made with autoCV

Main

header_img Brian M Schilder, PhD

Passionately pursuing transdisciplinary research to advance human health and knowledge.


Postdoctoral Research Scientist

Below are selected subsets of the full CV. -

Education

Imperial_small Imperial College London / The Alan Turing Institute

PhD; Computational Genomics & Machine Learning

London, UK

2024

Thesis: Multi-omic medicine: dissecting the cell type-specific and pleiotropic mechanisms underlying disease genomics at scale

GW The George Washington University / Georgetown University

MPhil; Comparative Neuroscience & Genomics

Washington, DC, USA

2017

Thesis: The evolution of the hippocampus and adult neurogenesis: novel insights into the origins of human memory

Brown Brown University / Princeton University

ScB; Neurological Diseases & Disorders

Providence, RI, USA

2011

Core Skills

Research

16+ years of deep expertise in genomics, AI, evolutionary biology and biomedicine. Strategically fuses concepts and methods across multiple domains.

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  • Publication record: 24 publications, 7 preprints and 14 awarded grants.
  • Reproducibility: Global leader in promoting and enabling reproducible scientific practices. Writes 100% reproducible manuscripts programmatically.
  • Bioinformatics: Created 45 Python and R packages to address key challenges in biological research.
  • High-performance computing: Highly parallelised analyses and AI model training (CPUs and GPUs).
  • Web development: 6+ websites, web apps, and interactive reports.

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AI & Machine Learning

Proficient in developing and deploying AI/ML models (PyTorch, tensorflow, Keras, sklearn and H2O) to solve complex biological problems. Applied examples include:

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  • Causal variant effect prediction: Used functional impact predictions from DNA sequence models (DeepSEA, Basenji, IMPACT) to validate SNPs prioritised with Bayesian fine-mapping.
  • Foundation models: Used transformer trained on >36M cells and protein sequence embeddings to uncover cell type-specific mechanisms of disease.
  • LLM knowledge extraction: Developed framework to extract quantitative metrics of phenotype severity from GPT-4.
  • Disease genomics embeddings: Developed VAE/graph models to reveal joint latent representation of genomic signatures across all diseases and phenotypes.
  • NLP: Created a suite of proprietary Python packages for advanced topic modelling of the PubMed literature to provide business intelligence to the world’s largest digital health, biotech, and pharma companies (as a consultant with 120/80 Group).
  • Tensor decomposition: Applied multi-condition factorisation to efficiently discover neurodegeneration-relevant trans-eQTLs

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Project Management

Efficient management strategies to define objectives, track progress and coordinate diverse teams.

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Soft Skills

Advances science through effective problem formulation, collaboration and communication.

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  • Problem formulation: Rapid hypothesis generation, project design, and creative problem solving.
  • Collaboration: Diverse and global collaborative networking.
  • Communication: Clear and concise distillation of complex results to a variety of audiences. Presented 25 conference posters.

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Publications

Chromatin Interaction and Histone Mark Signatures Associated With TBXT Expression in Metastatic Lung Cancer

Genes Chromosomes Cancer, (2025) (64):e70041; https://doi.org/10.1002/gcc.70041

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2025

RM Yaa, BM Schilder, RD Acemel, FC Wardle

rworkflows: automating reproducible practices for the R community

Nature Communications (2023) 15(149); https://doi.org/10.1038/s41467-023-44484-5

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2023

BM Schilder, AE Murphy, NG Skene
News
- Featured in Nature Communications Editors’ Highlights

Artificial intelligence for neurodegenerative experimental models

Alzheimer’s & Dementia (2023) http://doi.org/10.1002/alz.13479

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2023

SJ Marzi, BM Schilder, A Nott, C Sala Frigerio, S Willaime-Morawek, M Bucholc, DP Hanger,C James, PA Lewis, I Lourida, W Noble, F Rodriguez-Algarra, JA Sharif, M Tsalenchuk, LM Winchester, U Yaman, Z Yao, DEMON Network, JM Ranson, DJ Llewellyn

Artificial intelligence for dementia genetics and omics

Alzheimer’s & Dementia (2023) http://doi.org/10.1002/alz.13427

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2023

C Bettencourt, NG Skene, S Bandres-Ciga, E Anderson, LM Winchester, IF Foote, J Schwartzentruber, JA Botia, M Nalls, A Singleton, BM Schilder, J Humphrey, SJ Marzi, CE Toomey, A Al Kleifat, EL Harshfield, V Garfield, C Sandor, S Keat, S Tamburin, C Sala Frigerio, I Lourida, DEMON Network, JM Ranson, DJ Llewellyn

Artificial intelligence for dementia research methods optimization

Alzheimer’s & Dementia (2023) http://doi.org/10.1002/alz.13441

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2023

M Bucholc, C James, A Al Khleifat, A Badhwar, N Clarke, A Dehsarvi, CR Madan, SJ Marzi, C Shand, BM Schilder, S Tamburin, HM Tantiangco, I Lourida, DJ Llewellyn, JM Ranson

EpiCompare: R package for the comparison and quality control of epigenomic peak files

Bioinformatics Advances (2023) 13(1):vbad049; https://doi.org/10.1093/bioadv/vbad049

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2023

S Choi, BM Schilder, L Abbasova, AE Murphy, NG Skene

Dissecting the Shared Genetic Architecture of Suicide Attempt, Psychiatric Disorders, and Known Risk Factors

Biological Psychiatry (2022) 91(3):313-327; https://doi.org/10.1016/j.biopsych.2021.05.029

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2022

N Mullins, J Kang, AI Campos,…BM Schilder, et al. 

Multi-omic insights into Parkinson’s Disease: From genetic associations to functional mechanisms

Neurobiology of Disease (2021) 105580; https://doi.org/10.1016/j.nbd.2021.105580

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2021

BM Schilder, E Navarro, T Raj

Fine-Mapping of Parkinson’s Disease Susceptibility Loci Identifies Putative Causal Variants

Human Molecular Genetics (2021) ddab294; https://doi.org/10.1093/hmg/ddab294

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2021

BM Schilder, T Raj

echolocatoR: An Automated End-to-End Statistical and Functional Genomic Fine-Mapping Pipeline

Bioinformatics (2021) btab658; https://doi.org/10.1093/bioinformatics/btab658

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2021

BM Schilder, J Humphrey, T Raj

MungeSumstats: A Bioconductor Package for the Standardisation and Quality Control of Many GWAS Summary Statistics

Bioinformatics (2021) 37(23):4593-4596; https://doi.org/10.1093/bioinformatics/btab665

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2021

A Murphy, BM Schilder, NG Skene

Dysregulation of mitochondrial and proteo-lysosomal genes in Parkinson’s disease myeloid cells

Nature Genetics (2021) https://doi.org/10.1101/2020.07.20.212407

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2021

E Navarro, E Udine, K de Paiva Lopes, M Parks, G Riboldi, BM Schilder…T Raj
News
- Mount Sinai: Fighting Neurodegenerative Disorders (Mount Sinai Health System, 2019)

Phenome-wide and eQTL Associations of COVID-19 Genetic Risk Loci

iScience (2021) https://doi.org/10.1016/j.isci.2021.102550

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2021

C Moon, BM Schilder, T Raj, K-l Huang

Genome-Wide Association Study of over 40,000 Bipolar Disorder Cases Provides Novel Biological Insights

Nature Genetics (2021) 53:817-829; https://doi.org/10.1038/s41588-021-00857-4

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2021

N Mullins, AJ Forstner, KS O’Connell, B Coombes, JRI Coleman…BM Schilder… et al.
News
- Researchers identify 64 regions of the genome that increase risk for bipolar disorder (EurekAlert, 2021)
- Largest Bipolar Disorder Genetics Study Doubles Genetic Risk Factors (Nordic Society of Human Genetics and Precision Medicine, 2021)

Tensor decomposition of stimulated monocyte and macrophage gene expression profiles identifies neurodegenerative disease-specific trans-eQTLs

PLOS Genetics (2020) 16(9):e1008549; https://doi.org/10.1371/journal.pgen.1008549

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2020

S Ramdhani, E Navarro, E Udine, AG Efthymiou, BM Schilder, M Parks, A Goate, T Raj

Evolutionary shifts dramatically reorganized the human hippocampal complex

Journal of Comparative Neurology (2019) 528(17):3143-3170; https://doi.org/10.1002/cne.24822

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2019

BM Schilder, HM Petry, PR Hof

FAIRshake: Toolkit to Evaluate the Findability, Accessibility, Interoperability, and Reusability of Research Digital Resources

Cell Systems (2019) 9; https://doi.org/10.1016/j.cels.2019.09.011

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2019

D Clarke, L Wang, A Jones, M Wojciechowicz, D Torre, K Jagodnik, S Jenkins, P McQuilton, Z Flamholz, M Silverstein, BM Schilder…A Ma’ayan
News
- Chosen as ‘Featured Frontmatter’ article in Cell Systems

Geneshot: search engine for ranking genes from arbitrary text queries

Nucleic Acids Research (2019) 47(W1):W571-W577; https://doi.org/10.1093/nar/gkz393

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2019

A Lachmann, BM Schilder, ML Wojciechowicz, D Torre, MV Kuleshov, AB Keenan, A Ma’ayan
News
- Geneshot: Piercing the Literature to Identify and Predict Relevant Genes (University of Pittsburgh Health Sciences Library System Update, 2019)
- The Future of AI at the Hasso Plattner Institute for Digital Health at Mount Sinai (Mount Sinai Health System, 2020)

eXpression2Kinases (X2K) Web: linking expression signatures to upstream cell signaling networks

Nucleic Acids Research (2018) 46(W1):W171-W179; https://doi.org/10.1093/nar/gky458

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2018

DJB Clarke, MV Kuleshov, BM Schilder, D Torre, ME Duffy, AB Keenan, A Lachmann, AS Feldmann, GW Gundersen, MC Silverstein, Z Wang
News
- Mount Sinai Faculty Spotlight: Ma’ayan Lab (Mount Sinai Health System, 2018)

Defining elemental imitation mechanisms: A comparison of cognitive and motor-spatial imitation learning across object- and computer-based tasks

Journal of Cognition and Development (2015) 17(2):221-243; https://doi.org/10.1080/15248372.2015.1053483

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2015

F Subiaul, L Zimmerman, E Renner, BM Schilder, R Barr

Take the monkey and run

Journal of Neuroscience Methods (2015) 248:28-31; http://doi.org/10.1016/j.jneumeth.2015.03.023

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2015

KA Phillips, MK Hambright, K Hewes, BM Schilder, CN Ross, SD Tardif
News
- Monkeys on a Treadmill? A Conversation with Dr. Kimberley Phillips (Why Social Science?)

Becoming a high-fidelity - super - imitator: what are the contributions of social and individual learning?

Developmental Science (2014) 18(6):1025-1035; http://doi.org/10.1111/desc.12276

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2014

F Subiaul, EM Patterson, BM Schilder, E Renner, R Barr

Working memory constraints on imitation and emulation

Journal of Experimental Child Psychology (2014) 128:190-200; http://doi.org/10.1016/j.jecp.2014.07.005

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2014

F Subiaul, BM Schilder

Preprints

Gene expression patterns of the developing human face at single cell resolution reveal cell type contributions to normal facial variation and disease risk

bioRxiv (2025) https://www.biorxiv.org/content/10.1101/2025.01.18.633396v1

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2025

N Khouri-Farah, EW Winchester, BM Schilder, K Robinson, SW Curtis, NM Skene, E Leslie-Clarkson, J Cotney

Harnessing generative AI to annotate the severity of all phenotypic abnormalities within the Human Phenotype Ontology

medRxiv (2024) https://doi.org/10.1101/2024.06.10.24308475

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2024

KB Murphy, BM Schilder, NG Skene

Integrative multi-omics analysis of glial signatures associated with accelerated cognitive decline in Alzheimer’s disease

bioRxiv (2024) https://doi.org/10.1101/2024.08.27.24312641

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2024

E Schneegans, N Fancy, V Chau, TKD Cheung, E Adair, M Papageorgopoulou, BM Schilder, PM Matthews, JS Jackson

Fine-mapping genomic loci refines bipolar disorder risk genes

medRxiv (2023) https://www.medrxiv.org/content/10.1101/2024.02.12.24302716v1

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2023

M Koromina, A Ravi, G Panagiotaropoulou, BM Schilder, … S Ripke, T Raj, JRI Coleman, N Mullins
News
- Currently under journal review

Identification of cell type-specific gene targets underlying thousands of rare diseases and subtraits

medRxiv (2023) https://doi.org/10.1101/2023.02.13.23285820

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2023

KB Murphy, R Gordon-Smith, J Chapman, M Otani, BM Schilder, NG Skene

CUT&Tag recovers up to half of ENCODE ChIP-seq peaks

bioRxiv (2022) https://doi.org/10.1101/2022.03.30.486382

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2022

D Hu, L Abbasova, BM Schilder, A Nott, NG Skene, SJ Marzi

Research Experience

Postdoctoral Research Scientist

Cold Spring Harbor Laboratory (Simons Center for Quantitative Biology)

Cold Spring Harbor, NY, USA

- - 2024

  • Advancing deep learning applications in genomics and biomedicine in the laboratory of Dr. Peter Koo.
  • Developing a genomic foundation model to map complex genome-phenome relationships and make highly accurate, personalized disease risk predictions.

Lead Data Scientist

120/80 Group

New York, NY, USA

- - 2019

  • Offers data-driven consultation services to a wide portfolio of high-profile digital healthcare, pharmaceutical and biotech companies.
  • Developed a suite of proprietary softwares to extract customised business intelligence from the published literature to generate customised and interpretable reports to clients.
  • Provides clients guidance on strategic AI implementation, data analysis, publication and transparency.

Bioinformatician II

Icahn School of Medicine at Mount Sinai (Department of Neuroscience / Department of Neurology / Department of Genetics & Genomics / Ronald M. Loeb Center for Alzheimer’s Disease)

New York, NY, USA

2020 - 2018

  • Developed machine learning systems to integrate large-scale multi-omics datasets (e.g. whole-genome sequencing, bulk and single-cell RNA-seq, epigenomics, clinical data) to uncover the molecular mechanisms underlying neurodegenerative diseases (e.g. Alzheimer’s, Parkinson’s, ALS).
  • Computationally identified specific disease-causal variants, pathways and cell-types for subsequent functional wet lab validation (e.g. CRISPR-cas9 editing in patient-derived cell cultures, iPSCs and cerebral organoids).

Bioinformatician II

Icahn School of Medicine at Mount Sinai (Department of Pharmacological Sciences)

New York, NY, USA

2018 - 2017

  • Conducted computational systems biology research. Integrated and analyzed large-scale genomic and biomedical data (e.g. Python, R, JavaScript).
  • Developed evolutionary algorithm to optimize gene network kinase regulator prediction (eXpression2Kinases).
  • Developed and deployed computational tools, software, databases and web applications for basic and clinical research, resulting in 3 peer-reviewed publications.

Research Assistant

The George Washington University (Department of Anthropology)

Washington, DC, USA

2013 - 2011

  • Performed dissection, histology, microscopy and quantitative stereology in post-mortem primate brain tissues.
  • Trained junior and senior personnel on lab protocols.

Senior Lab Manager

The George Washington University (Department of Speech, Language & Hearing Sciences)

Washington, DC, USA

2013 - 2011

  • Organized and trained dozens of undergraduates to conduct weekly cognitive development research; designed and/or directly contributed to over 15 research projects in two years.

Grants

Total (all grants): $3,049,872
Total (as primary applicant): $311,382

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